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This work scrutinises the policy shift in Germany with the change in leitmotif from biotechnology to bioeconomy and examines the associated implications at various levels. The emergence and implementation of innovation policy funding programmes show that the policy transition did not follow a linear sequence. Neither excessive prioritisation nor neglect of a selected sector can be confirmed in this analysis. However, the policy shift from biotechnology to bioeconomy has not only consequences in terms of its content, but also affects the spatial distribution of R&D funding. Against the background of existing polarisation tendencies and the growing acknowledgement of inclusive innovation policy approaches, this study examines the importance the bioeconomy can assume in the reduction of regional disparities. In ‘organisationally thick’ regions, depending on the involvement of private actors, specialisation and regional branching can be observed. It is found that, for rural regions, the bioeconomy can be an appropriate tool for regional development, since other industries are often not present.